Estimate the diversity of species from abundance or probability data and a phylogenetic tree. Several estimators are available to deal with incomplete sampling.
div_phylo(x, tree, q = 1, ...)
# S3 method for numeric
div_phylo(
x,
tree,
q = 1,
normalize = TRUE,
estimator = c("UnveilJ", "ChaoJost", "ChaoShen", "GenCov", "Grassberger", "Marcon",
"UnveilC", "UnveiliC", "ZhangGrabchak", "naive", "Bonachela", "Holste"),
level = NULL,
probability_estimator = c("Chao2015", "Chao2013", "ChaoShen", "naive"),
unveiling = c("geometric", "uniform", "none"),
richness_estimator = c("jackknife", "iChao1", "Chao1", "naive"),
jack_alpha = 0.05,
jack_max = 10,
coverage_estimator = c("ZhangHuang", "Chao", "Turing", "Good"),
as_numeric = FALSE,
...,
check_arguments = TRUE
)
# S3 method for species_distribution
div_phylo(
x,
tree,
q = 1,
normalize = TRUE,
estimator = c("UnveilJ", "ChaoJost", "ChaoShen", "GenCov", "Grassberger", "Marcon",
"UnveilC", "UnveiliC", "ZhangGrabchak", "naive", "Bonachela", "Holste"),
level = NULL,
probability_estimator = c("Chao2015", "Chao2013", "ChaoShen", "naive"),
unveiling = c("geometric", "uniform", "none"),
richness_estimator = c("jackknife", "iChao1", "Chao1", "naive"),
jack_alpha = 0.05,
jack_max = 10,
coverage_estimator = c("ZhangHuang", "Chao", "Turing", "Good"),
gamma = FALSE,
...,
check_arguments = TRUE
)An object, that may be a numeric vector containing abundances or probabilities, or an object of class abundances or probabilities.
An ultrametric, phylogenetic tree. May be an object of class phylo_divent, ape::phylo, ade4::phylog or stats::hclust.
The order of diversity.
Unused.
If TRUE, phylogenetic is normalized: the height of the tree is set to 1.
An estimator of asymptotic diversity.
The level of interpolation or extrapolation.
It may be a sample size (an integer) or a sample coverage
(a number between 0 and 1).
If not NULL, the asymptotic estimator is ignored.
A string containing one of the possible estimators of the probability distribution (see probabilities). Used only for extrapolation.
A string containing one of the possible unveiling methods to estimate the probabilities of the unobserved species (see probabilities). Used only for extrapolation.
An estimator of richness to evaluate the total number of species, see div_richness. Used for interpolation and extrapolation.
The risk level, 5% by default, used to optimize the jackknife order.
The highest jackknife order allowed. Default is 10.
An estimator of sample coverage used by coverage.
If TRUE, a number or a numeric vector is returned rather than a tibble.
If TRUE, the function arguments are verified.
Should be set to FALSE to save time when the arguments have been checked elsewhere.
If TRUE, \(\gamma\) diversity, i.e. diversity of the metacommunity, is computed.
A tibble with the site names, the estimators used and the estimated diversity
Bias correction requires the number of individuals. See div_hill for estimators.
Entropy can be estimated at a specified level of interpolation or extrapolation, either a chosen sample size or sample coverage (Chao et al. 2014) , rather than its asymptotic value. See accum_tsallis for details.
Chao A, Gotelli NJ, Hsieh TC, Sander EL, Ma KH, Colwell RK, Ellison AM (2014). “Rarefaction and Extrapolation with Hill Numbers: A Framework for Sampling and Estimation in Species Diversity Studies.” Ecological Monographs, 84(1), 45--67. doi:10.1890/13-0133.1 .
div_phylo(paracou_6_abd, tree = paracou_6_taxo, q = 2)
#> # A tibble: 4 × 4
#> site weight estimator diversity
#> <chr> <dbl> <chr> <dbl>
#> 1 subplot_1 1.56 UnveilJ 17.7
#> 2 subplot_2 1.56 UnveilJ 21.3
#> 3 subplot_3 1.56 UnveilJ 20.5
#> 4 subplot_4 1.56 UnveilJ 16.4
# At 80% coverage
div_phylo(paracou_6_abd, tree = paracou_6_taxo, q = 2, level = 0.8)
#> # A tibble: 4 × 4
#> site weight estimator diversity
#> <chr> <dbl> <chr> <dbl>
#> 1 subplot_1 1.56 UnveilJ 14.4
#> 2 subplot_2 1.56 UnveilJ 17.7
#> 3 subplot_3 1.56 UnveilJ 16.7
#> 4 subplot_4 1.56 UnveilJ 14.0
# Gamma entropy
div_phylo(paracou_6_abd, tree = paracou_6_taxo, q = 2, gamma = TRUE)
#> # A tibble: 1 × 3
#> site estimator diversity
#> <chr> <chr> <dbl>
#> 1 Metacommunity UnveilJ 19.7